From 3ee3ca20c8fee3a3b3a8fd4d1c55610609f505e8 Mon Sep 17 00:00:00 2001
From: Mohammed Faizal Eeman Mootor
 <68152431+Faizal-Eeman@users.noreply.github.com>
Date: Thu, 3 Aug 2023 09:45:32 -0700
Subject: [PATCH] Fix pulling submodule in release `6.0.0-rc.1` (#113)

* Update submodule pipeline-Nextflow-config

* Update CHANGELOG.md

* update PR template

* Update CHANGELOG.md

* Update CHANGELOG.md

---------

Co-authored-by: Mootor <mmootor@ip-0A125250.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>
---
 .github/PULL_REQUEST_TEMPLATE.md  | 6 +++---
 CHANGELOG.md                      | 3 ++-
 external/pipeline-Nextflow-config | 2 +-
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index cca43dc..78eed49 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,12 +8,12 @@
 
 - DNA A-mini
     - sample:    <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 -->
-    - input csv: <!-- path/to/input.csv -->
+    - input yaml: <!-- path/to/input.yaml -->
     - config:    <!-- path/to/xxx.config -->
     - output:    <!-- path/to/output -->
 - DNA A-full
     - sample:    <!-- e.g. A-full S2.T-1, A-full S2.T-n1 -->
-    - input csv: <!-- path/to/input.csv -->
+    - input yaml: <!-- path/to/input.yaml -->
     - config:    <!-- path/to/xxx.config -->
     - output:    <!-- path/to/output -->
 
@@ -36,4 +36,4 @@ already, or do not wish to be listed. (*This acknowledgement is optional.*)
 
 - [ ] I have updated the version number in the `metadata.yaml` and `manifest` block of the `nextflow.config` file following [semver](https://semver.org/), or the version number has already been updated. (*Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.*)
 
-- [ ] I have tested the pipeline on at least one A-mini sample with `algorithm = ['delly', 'manta']`. The paths to the test config files and output directories are attached above. 
+- [ ] I have tested the pipeline on at least one A-mini sample with `algorithm = ['delly', 'manta']`. The paths to the test config files and output directories are attached above.
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ca6539e..84ec80f 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,9 +16,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - YAML input
 
 ### Changed
+- Update to latest commit of `pipeline-Nextflow-config``
 - Update pipeline SVG
 - Update YAML input and tests in `README.md`
-- Update Pipeval to `v4.0.0-rc.2`
+- Update PipeVal to `v4.0.0-rc.2`
 - Parse sample ID from tumor BAM for output directory naming
 - Update `README.md` to clarify adjustable parameters and note lab default values
 
diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config
index cb9a702..c77aeca 160000
--- a/external/pipeline-Nextflow-config
+++ b/external/pipeline-Nextflow-config
@@ -1 +1 @@
-Subproject commit cb9a702a2e4f04162529315b87cc19149866df65
+Subproject commit c77aecab50304e9c7c8cd20d00fd5e57b89e8ad2